Primers pairs used in quantitative real-time RT-PCR.

1<p>ADAMTS8, ADAM metallopeptidase with thrombospondin type 1 motif, 8; ALDOA, aldolase A, fructose-bisphosphate; B2M, beta-2-microglobulin; CEBPA, CCAAT/enhancer binding protein (C/EBP), alpha; CPT1B, carnitine palmitoyltransferase 1B (muscle); DGAT2, diacylglycerol O-acyltransferase 2; RYR1, ryanodine receptor 1 (skeletal); TBP1, TATA box binding protein; TGFB1, transforming growth factor, beta 1.</p>2<p>Accession number of the Sus scrofa sequence used to design primers.</p>3<p>Gene used as reference for normalization.</p

Genes overexpressed in <i>Longissimus</i> muscle (n = 10).

1<p>Only genes with at least one associated GO BP term are presented in the table.</p>2<p>Differentially expressed genes were clustered using GO BP terms semantic similarity between genes as distance, to group functionally similar genes together.</p>3<p>Fold Change is expressed as the expression ratio of <i>Longissimus</i> to <i>Semimembranosus</i> samples.</p>4<p>Benjamini and Hochberg adjusted P value.</p>5<p>Unique identifier and gene ontology term in the GO database (<a href="http://www.geneontology.org/" target="_blank">http://www.geneontology.org/</a>).</p

Validation of seven microarray differentially expressed genes between Longissimus (LM) and Semimembranosus (SM) muscles by quantitative RT-PCR.

<p>mRNA level is expressed using arbitrary units. Quantitative RT-PCR expression levels (LM = 8, SM = 8) were normalized to the expression of beta 2 microglobulin (<i>B2M</i>), TATAbox binding protein (<i>TBP</i>) and <i>18S</i> using geNorm algorithm. Microarray adjusted means for LM and SM (LM = 90; SM = 90) were calculated using least square means for the muscle effect. Data are expressed as means±s.d. Statistical significances are reported below the plot as Benjamini and Hochberg adjusted P-value for microarray data and as Student t-test P value for q RT-PCR. Fold change ratio is expressed as the expression ratio of LM to SM when genes are overrepresented in LM and as the expression ratio of SM to LM when genes are overrepresented in SM.</p

Genes overexpressed in <i>Semimembranosus</i> muscle (n = 10).

1<p>Only genes with at least one associated GO BP term are presented in the table.</p>2<p>Differentially expressed genes were clustered using GO BP terms semantic similarity between genes as distance, to group functionally similar genes together.</p>3<p>Fold Change is expressed as the expression ratio of <i>Semimembranosus</i> to <i>Longissimus</i> samples.</p>4<p>Benjamini and Hochberg adjusted P value.</p>5<p>Unique identifier and gene ontology term in the GO database (<a href="http://www.geneontology.org/" target="_blank">http://www.geneontology.org/</a>).</p

Relevant biological processes significantly enriched in clustered differentially expressed genes.

1<p>Differentially expressed genes were clustered using GO BP terms semantic similarity between genes as distance, to group functionally similar genes together.</p>2<p>Cluster enrichment score (ES).</p>3<p>Unique identifier and gene ontology term in the GO database (<a href="http://www.geneontology.org/" target="_blank">http://www.geneontology.org/</a>).</p>4<p>n_G, number of genes in the category.</p>5<p>Benjamini and Hochberg adjusted P value.</p

Hierarchical clustering of differentially expressed genes according to their GO BP terms semantic similarity.

<p>Annotated differentially expressed genes with a muscle fold change above 1.5 were clustered based on their functional annotation (GO BP) semantic similarity. Hierarchical clustering was performed using “1-semantic similarity” as distance between two genes (similar genes have a distance close to zero) to identify clusters of genes sharing BP terms. Five clusters were identified. Cluster 1 comprised 98 genes highly expressed in SM and 44 in LM. Cluster 2 included 73 highly expressed genes in SM and 102 in LM. Cluster 3 contained 43 highly expressed genes in SM and 84 in LM. Cluster 4 comprised 288 genes overexpressed in SM and 192 in LM. Cluster 5 involved 90 overexpressed genes in SM and 33 overexpressed genes in LM.</p

Relevant biological pathways significantly enriched in clustered differentially expressed genes.

1<p>Differentially expressed genes were clustered using GO BP terms semantic similarity between genes as distance, to group functionally similar genes together.</p>2<p>Cluster enrichment score (ES).</p>3<p>n_G, number of genes in the category.</p>4<p>Benjamini and Hochberg adjusted P value.</p

Gene expression ratio between muscles.

<p>Muscle fold change ratio is expressed as the expression ratio of <i>Longissimus</i> (LM) to <i>Semimembranosus</i> (SM) samples when genes are highly expressed in <i>Longissimus</i> and as the expression ratio of SM to LM samples when genes are highly expressed in <i>Semimembranosus</i>.</p